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A pipeline for sample tagging of whole genome bisulfite sequencing data using genotypes of whole genome sequencing
BackgroundIn large-scale high-throughput sequencing projects and biobank construction, sample tagging is essential to prevent sample mix-ups. Despite...
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Analyzing somatic mutations by single-cell whole-genome sequencing
Somatic mutations are the cause of cancer and have been implicated in other, noncancerous diseases and aging. While clonally expanded mutations can...
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Whole-genome sequencing in medicinal plants: current progress and prospect
Advancements in genomics have dramatically accelerated the research on medicinal plants, and the development of herbgenomics has promoted the...
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What Whole Genome Sequencing Has Told Us About Pathogenic Vibrios
When the first microbial genome sequences were published just 20 years ago, our understanding regarding the microbial world changed dramatically. The...
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Optimized whole-genome sequencing workflow for tumor diagnostics in routine pathology practice
Two decades after the genomics revolution, oncology is rapidly transforming into a genome-driven discipline, yet routine cancer diagnostics is still...
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Use of Whole Genome Sequencing for Mycobacterium tuberculosis Complex Antimicrobial Susceptibility Testing
Whole genome sequencing (WGS) is becoming an important diagnostic tool for antimicrobial susceptibility testing of Mycobacterium tuberculosis complex...
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DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus
BackgroundThe increasing burden of dengue virus on public health due to more explosive and frequent outbreaks highlights the need for improved...
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Caveats for Watermelon Whole Genome Sequencing
Watermelon is a highly important vegetable crop species worldwide, with its abundance of genetic resources aiding in identifying mechanisms and...
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Use of Whole Genome Sequencing for Mycobacterium tuberculosis Complex Antimicrobial Susceptibility Testing: From Sequence Data to Resistance Profiles
Whole genome sequencing of Mycobacterium tuberculosis complex (MTBC) isolates has been shown to provide accurate predictions for resistance and...
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Cost-effective library preparation for whole genome sequencing with feather DNA
Samples from avian species of high conservation concern are often low in total genomic DNA (gDNA). Feathers are collected more frequently than blood,...
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Genetic characterization of tetracycline-resistant Staphylococcus aureus with reduced vancomycin susceptibility using whole-genome sequencing
This study aimed to analyze the genetic characteristics of Staphylococcus aureus with reduced vancomycin susceptibility (RVS-SA). Whole-genome...
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Whole-genome sequencing reveals genomic diversity and selection signatures in **a’nan cattle
BackgroundThe crossbreeding of specialized beef cattle breeds with Chinese indigenous cattle is a common method of genetic improvement. **a’nan...
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Mutation Map** and Identification by Whole-Genome Sequencing
Geneticists approach biology with a simple question: which genes are required for the pathway or process of interest? Classical genetic screens (aka...
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Fast and sensitive validation of fusion transcripts in whole-genome sequencing data
BackgroundIn cancer, genomic rearrangements can create fusion genes that either combine protein-coding sequences from two different partner genes or...
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HostSeq: a Canadian whole genome sequencing and clinical data resource
HostSeq was launched in April 2020 as a national initiative to integrate whole genome sequencing data from 10,000 Canadians infected with SARS-CoV-2...
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Towards reliable whole genome sequencing for outbreak preparedness and response
BackgroundTo understand the dynamics of infectious diseases, genomic epidemiology is increasingly advocated, with a need for rapid generation of...
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Comparative genomics of four lactic acid bacteria identified with Vitek MS (MALDI-TOF) and whole-genome sequencing
Lactic acid bacteria (LAB) can be used as a probiotic or starter culture in dairy, meat, and vegetable fermentation. Therefore, their isolation and...
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ERStruct: a fast Python package for inferring the number of top principal components from whole genome sequencing data
BackgroundLarge-scale multi-ethnic DNA sequencing data is increasingly available owing to decreasing cost of modern sequencing technologies....
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Genome-wide association study considering genotype-by-environment interaction for productive and reproductive traits using whole-genome sequencing in Nellore cattle
BackgroundThe genotype-by-environment interaction (GxE) in beef cattle can be investigated using reaction norm models to assess environmental...
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Identification of Novel Induced Mutations in Seed and Vegetatively Propagated Plants from Reduced Representation or Whole Genome Sequencing Data
Treatment of plants with chemical mutagens results primarily in the production of novel single nucleotide variants. Mutagenesis is a mostly random...